James Lindesay

Surface-state origin for the blueshifted emission in anodically etched porous silicon carbide

Anodic etching of SiC yields a highly monodisperse distribution of nanometer dimension porous structures which extend to a significant depth. Cathodoluminescence (CL) studies of the porous layers yield luminescence peaks in the UV region, above the band gap energy of bulk SiC. Higher etching current densities produce porous silicon carbide (PSiC) with peak CL emission wavelengths deeper in the ultraviolet. Photoluminescence (PL) is also blueshifted in anodically etched PSiC, although not to the extent of the CL emission, suggesting that different emissive states are accessed in CL and PL. Raman investigations of the polar A1 LO mode, which couples strongly to the macroscopic electric field accompanying the LO phonon, were conducted in an attempt to discern whether quantum confinement effects could effectively explain the blueshifted emission. The principal feature of the Raman spectra was a significant low-frequency shoulder on the A1 LO mode, the magnitude of which correlates with the magnitude of the bl...

Coordinates with Non-Singular Curvature for a Time Dependent Black Hole Horizon

A naive introduction of a dependency of the mass of a black hole on the Schwarzschild time coordinate results in singular behavior of curvature invariants at the horizon, violating expectations from complementarity. If instead a temporal dependence is introduced in terms of a coordinate akin to the river time representation, the Ricci scalar is nowhere singular away from the origin. It is found that for a shrinking mass scale due to evaporation, the null radial geodesics that generate the horizon are slightly displaced from the coordinate singularity. In addition, a changing horizon scale significantly alters the form of the coordinate singularity in diagonal (orthogonal) metric coordinates representing the space-time. A Penrose diagram describing the growth and evaporation of an example black hole is constructed to examine the evolution of the coordinate singularity.

Construction of a Penrose diagram for a spatially coherent evaporating black hole

A Penrose diagram is constructed for an example black hole that evaporates at a steady rate as measured by a distant observer, until the mass vanishes, yielding a final state Minkowski spacetime. Coordinate dependences of significant features, such as the horizon and coordinate anomalies, are clearly demonstrated on the diagram. The large-scale causal structure of the spacetime is briefly discussed.

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases.

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzymes displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism.

Penrose diagram for a transient black hole

A Penrose diagram is constructed for a spatially coherent black hole that smoothly begins an accretion, and then excretes symmetrically as measured by a distant observer, with the initial and final states described by a metric of the Minkowski form. Coordinate curves on the diagram are computationally derived. Causal relationships between spacetime regions are briefly discussed. The life cycle of the black hole demonstrably leaves asymptotic observers in an unaltered Minkowski spacetime of uniform conformal scale.

Exploration of the Physics of Spherically Symmetric Dynamic Horizons

Geometries with horizons offer insights into relationships between general relativity and quantum physics. For static spherically symmetric space‐times, the event horizon is coincident with a coordinate anomaly that introduces complications in descriptions of near horizon physics. Naive introduction of dynamics using coordinates with anomalous behavior coincident with the horizon also introduces invariant singular physical content at that horizon. However, the introduction of a temporal coordinate that is non‐orthogonal to spatial coordinates near the horizon, but asymptotically orthogonal, provides a dynamic description without singular physical content at the horizon itself. Penrose diagrams will be presented exhibiting temporal dependencies for accreting and evaporating black holes, and near horizon light‐like trajectories will be examined. In addition, the quantum mechanics of simple quantum fields will be explored. Finally, a two‐fluid cosmology will be suggested to describe dynamic coherent aspects ...

CMB fluctuation amplitude from dark energy partitions

Abstract It is assumed that the dark energy observed today is frozen as a result of a phase transition involving the source of that energy. Postulating that the dark energy decoherence which results from this phase transition drives statistical variations in the energy density specifies a class of cosmological models in which the cosmic microwave background (CMB) fluctuation amplitude at last scattering is approximately 10−5.

A new biophysical metric for interrogating the information content in human genome sequence variation: Proof of concept.

The 21st century emergence of genomic medicine is shifting the paradigm in biomedical science from the population phenotype to the individual genotype. In characterizing the biology of disease and health disparities in population genetics, human populations are often defined by the most common alleles in the group. This definition poses difficulties when categorizing individuals in the population who do not have the most common allele(s). Various epidemiological studies have shown an association between common genomic variation, such as single nucleotide polymorphisms (SNPs), and common diseases. We hypothesize that information encoded in the structure of SNP haploblock variation in the human leukocyte antigen-disease related (HLA-DR) region of the genome illumines molecular pathways and cellular mechanisms involved in the regulation of host adaptation to the environment. In this paper we describe the development and application of the normalized information content (NIC) as a novel metric based on SNP haploblock variation. The NIC facilitates translation of biochemical DNA sequence variation into a biophysical quantity derived from Boltzmanns canonical ensemble in statistical physics and used widely in information theory. Our normalization of this information metric allows for comparisons of unlike, or even unrelated, regions of the genome. We report here NIC values calculated for HLA-DR SNP haploblocks constructed by Haploview, a product of the International Haplotype Map Project. These haploblocks were scanned for potential regulatory elements using ConSite and miRBase, publicly available bioinformatics tools. We found that all of the haploblocks with statistically low NIC values contained putative transcription factor binding sites and microRNA motifs, suggesting correlation with genomic regulation. Thus, we were able to relate a mathematical measure of information content in HLA-DR SNP haploblocks to biologically relevant functional knowledge embedded in the structure of DNA sequence variation. We submit that NIC may be useful in analyzing the regulation of molecular pathways involved in host adaptation to environmental pathogens and in decoding the functional significance of common variation in the human genome.

Nonperturbative, Unitary Quantum-Particle Scattering Amplitudes from Three-Particle Equations

We here use our nonperturbative, cluster decomposable relativistic scattering formalism to calculate photon–spinor scattering, including the related particle–antiparticle annihilation amplitude. We start from a three-body system in which the unitary pair interactions contain the kinematic possibility of single quantum exchange and the symmetry properties needed to identify and substitute antiparticles for particles. We extract from it a unitary two-particle amplitude for quantum–particle scattering. We verify that we have done this correctly by showing that our calculated photon–spinor amplitude reduces in the weak coupling limit to the usual lowest order, manifestly covariant (QED) result with the correct normalization. That we are able to successfully do this directly demonstrates that renormalizability need not be a fundamental requirement for all physically viable models.

Quantum behaviors on an excreting black hole

Often, geometries with horizons offer insights into the intricate relationships between general relativity and quantum physics. However, some subtle aspects of gravitating quantum systems might be difficult to ascertain using static backgrounds, since quantum mechanics incorporates dynamic measurability constraints (such as the uncertainty principle, etc). For this reason, the behaviors of quantum systems on a dynamic black hole background are explored in this paper. The velocities and trajectories of representative outgoing, ingoing and stationary classical particles are calculated and contrasted, and the dynamics of simple quantum fields (both massless and massive) on the spacetime are examined. Invariant densities associated with the quantum fields are exhibited on the Penrose diagram that represents the excreting black hole. Furthermore, a generic approach for the consistent mutual gravitation of quanta in a manner that reproduces the given geometry is developed. The dynamics of the mutually gravitating quantum fields are expressed in terms of the affine parameter that describes local motions of a given quantum type on the spacetime. Algebraic equations that relate the energy–momentum densities of the quantum fields to Einsteins tensor can then be developed. An example mutually gravitating system of macroscopically coherent quanta along with a core gravitating field is demonstrated. Since the approach is generic and algebraic, it can be used to represent a variety of systems with specified boundary conditions.